This project will sequence and annotate the genomes of the mouse pneumonitis (MoPn) strain of Chlamydia trachomatis and a human strain of Chlamydia pneumoniae. Chlamydiae are ideal candidates for genome sequencing projects because of their medical importance, relatively small genome size and the lack of contemporary genetic approaches for their study. The genome sizes of mouse C. trachomatis and human C. pneumoniae are each estimated to be just over 1 Mbp in size. Complete DNA sequence will be obtained by sequencing the ends of inserts in approximately 15,000 plasmid clones per genome. Also, the ends of approximately 200 lambda clones for each species will be sequenced to provide resources for closures, confirm genome assembly, and provide a mapped set of clones spanning the genome. Similarities between chlamydial and known genes in sequence databases will be identified by computer searches. This proposal complements the work of Dr. R. Stephens (University of California, Berkeley) and the Stanford Chlamydia Group who are sequencing human strains of C. trachomatis (serovars D and L2). Short of primate studies, there is no good animal model to evaluate the biology of chlamydial genes from human strains of C. trachomatis. Identification of interesting genes in MoPn will allow targeting of homologous genes from human C. trachomatis genomes. In addition, MoPn produces natural infection in mice and has a well-characterized immunobiology. The investigators anticipate that it will be faster to identify genes from human strains of C. trachomatis. In this way, MoPn gene sequencing should facilitate more efficient application of genomic sequence knowledge derived from human C. trachomatis strains. The rationale for determining the genomic sequence of C. pneumoniae is more directly related to its application for human infection biology and should dramatically accelerate studies on the potential relationship between C. pneumoniae vascular infection and atherosclerosis. Comparison of the four chlamydial genomes may also define the molecular basis for species specificity and tissue tropism.